The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis
Resolution: 1.85 Å
EM Method: Single-particle
Fitted PDBs: 8uem
Q-score: 0.777
Kropp A, Gillett DL, Venugopal H, Gonzalvez MA, Lingford JP, Jain S, Barlow CK, Zhang J, Greening C, Grinter R
Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01836-0 Pubmed: 39881213 ]
- Carbon monoxide dehydrogenase (large chain), coxl (85 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cu(i)-s-mo(iv)(=o)oh cluster (224 Da, Ligand)
- Mocu carbon monoxide dehydrogenase (mocu-codh) (270 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Water (18 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Carbon monoxide dehydrogenase medium chain (31 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- [2fe-2s] binding domain protein (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Pterin cytosine dinucleotide (696 Da, Ligand)
Cryo-EM structure of PqqU with ligand PQQ
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 9c4o
Q-score: 0.74
Munder F, Voutsinos M, Hantke K, Venugopal H, Grinter R
To Be Published
- Pyrroloquinoline quinone (330 Da, Ligand)
- Water (18 Da, Ligand)
- Pyrroloquinoline quinone transporter (78 kDa, Protein from Escherichia coli BW25113)
- Calcium ion (40 Da, Ligand)
- Complex of pqqu with pqq (78 kDa, Complex from Escherichia coli BW25113)
Resolution: 2.19 Å
EM Method: Single-particle
Fitted PDBs: 7utd
Q-score: 0.496
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ DOI: doi:10.1038/s41586-023-05781-7 Pubmed: 36890228 ]
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Type 2 [nife]-hydrogenase huc membrane adapter subunit (6 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Hydrogenase-2, small subunit (39 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nickel (iii) ion (58 Da, Ligand)
Resolution: 1.67 Å
EM Method: Single-particle
Fitted PDBs: 7uur
Q-score: 0.837
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ DOI: doi:10.1038/s41586-023-05781-7 Pubmed: 36890228 ]
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Hydroxide ion (17 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Menadione (172 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nickel (iii) ion (58 Da, Ligand)
Resolution: 8.0 Å
EM Method: Single-particle
Fitted PDBs: 7uus
Q-score: 0.104
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ DOI: doi:10.1038/s41586-023-05781-7 Pubmed: 36890228 ]
- [nife]-hydrogenase huc membrane associated subunit (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Magnesium ion (24 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe3-s4 cluster (295 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Hydrogenase-2, small subunit (39 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nickel (iii) ion (58 Da, Ligand)
Resolution: 1.52 Å
EM Method: Single-particle
Fitted PDBs: 8dqv
Q-score: 0.857
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
Nature (2023) 615 pp. 541-547 [ DOI: doi:10.1038/s41586-023-05781-7 Pubmed: 36890228 ]
- Complex of the type 2 [nife]-hydrogenase huc from mycobacterium smegmatis (833 kDa, Complex from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Hydrogenase-2, large subunit (57 kDa, Protein from Mycolicibacterium smegmatis)
- Hydrogenase-2, small subunit (35 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- Fe3-s4 cluster (295 Da, Ligand)
- Carbonmonoxide-(dicyano) iron (135 Da, Ligand)
- Menadione (172 Da, Ligand)
- Nickel (iii) ion (58 Da, Ligand)
- Oxygen atom (15 Da, Ligand)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6xgq
Q-score: 0.488
Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F
Nat Commun (2020) 11 pp. 3748-3748 [ DOI: doi:10.1038/s41467-020-17505-w Pubmed: 32719311 ]
- Ysd1_17 (39 kDa, Protein from Bacteriophage sp.)
- Bacteriophage sp. (22 MDa, Virus from Bacteriophage sp.)
- Ysd1_16 (14 kDa, Protein from Bacteriophage sp.)
Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 6xgr
Q-score: 0.493
Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F
Nat Commun (2020) 11 pp. 3748-3748 [ DOI: doi:10.1038/s41467-020-17505-w Pubmed: 32719311 ]
- Ysd1_22 major tail protein (40 kDa, Protein from Bacteriophage sp.)
- Bacteriophage sp. (56 MDa, Virus from Bacteriophage sp.)